public class ImmoniumIon extends Ion
Ion.IonType
Modifier and Type | Field and Description |
---|---|
char |
aa
The amino acid that can generate this ion as single letter code.
|
static ImmoniumIon |
ALANINE
Alanine immonium ion.
|
static ImmoniumIon |
ARGININE
Arginine immonium ion.
|
static ImmoniumIon |
ASPARAGINE
Asparagine immonium ion.
|
static ImmoniumIon |
ASPARTIC_ACID
Aspartic acid immonium ion.
|
static ImmoniumIon |
CYSTEINE
Cysteine immonium ion.
|
static ImmoniumIon |
GLUTAMIC_ACID
Glutamic acid immonium ion.
|
static ImmoniumIon |
GLUTAMINE
Glutamine immonium ion.
|
static ImmoniumIon |
GLYCINE
Glycine immonium ion.
|
static ImmoniumIon |
HISTIDINE
Histidine immonium ion.
|
static ImmoniumIon |
ISOLEUCINE
Isoleucine immonium ion.
|
static ImmoniumIon |
LEUCINE
Leucine immonium ion.
|
static ImmoniumIon |
LYSINE
Lysine immonium ion.
|
static ImmoniumIon |
METHIONINE
Methionine immonium ion.
|
static ImmoniumIon |
PHENYLALANINE
Phenylananine immonium ion.
|
static ImmoniumIon |
PROLINE
Proline immonium ion.
|
static ImmoniumIon |
PYRROLYSINE
Pyrrolysine immonium ion.
|
static ImmoniumIon |
SELENOCYSTEINE
Selenocysteine immonium ion.
|
static ImmoniumIon |
SERINE
Serine immonium ion.
|
static ImmoniumIon |
THREONINE
Threonine immonium ion.
|
static ImmoniumIon |
TRYPTOPHAN
Tryptophan immonium ion.
|
static ImmoniumIon |
TYROSINE
Tyrosine immonium ion.
|
static ImmoniumIon |
VALINE
Valine immonium ion.
|
atomChain, theoreticMass, theoreticMass1, type
Modifier and Type | Method and Description |
---|---|
static ImmoniumIon |
getImmoniumIon(char residue)
Returns the immonium ion produced by the given amino acid.
|
static ImmoniumIon |
getImmoniumIon(int subType)
Returns the immonium ion corresponding to the given subtype.
|
String |
getName()
Returns the name of the ion.
|
NeutralLoss[] |
getNeutralLosses()
Returns the possible neutral losses of this ion type.
|
static ArrayList<Integer> |
getPossibleSubtypes()
Returns an arraylist of possible subtypes.
|
CvTerm |
getPrideCvTerm()
Returns the CV term adapted to the fragment ion.
|
CvTerm |
getPsiMsCvTerm()
Returns the CV term adapted to the fragment ion.
|
int |
getSubType()
Returns the ion subtype.
|
String |
getSubTypeAsString()
Returns the subtype as string.
|
boolean |
isSameAs(Ion anotherIon)
Returns a boolean indicating whether the ion is the same as another ion.
|
getAtomicComposition, getGenericIon, getGenericIon, getImplementedIonTypes, getNeutralLossesAsString, getNeutralLossesAsString, getPossibleSubtypes, getTheoreticMass, getTheoreticMz, getType, getTypeAsString, getTypeAsString, hasNeutralLosses, setAtomicComposition, setTheoreticMass
addUrParam, clearParametersMap, getUrParam, removeUrParam
public static final ImmoniumIon ALANINE
public static final ImmoniumIon ARGININE
public static final ImmoniumIon ASPARAGINE
public static final ImmoniumIon ASPARTIC_ACID
public static final ImmoniumIon CYSTEINE
public static final ImmoniumIon GLUTAMIC_ACID
public static final ImmoniumIon GLUTAMINE
public static final ImmoniumIon GLYCINE
public static final ImmoniumIon HISTIDINE
public static final ImmoniumIon ISOLEUCINE
public static final ImmoniumIon LEUCINE
public static final ImmoniumIon LYSINE
public static final ImmoniumIon METHIONINE
public static final ImmoniumIon PHENYLALANINE
public static final ImmoniumIon PROLINE
public static final ImmoniumIon SELENOCYSTEINE
public static final ImmoniumIon SERINE
public static final ImmoniumIon THREONINE
public static final ImmoniumIon TRYPTOPHAN
public static final ImmoniumIon TYROSINE
public static final ImmoniumIon VALINE
public static final ImmoniumIon PYRROLYSINE
public final char aa
public static ImmoniumIon getImmoniumIon(int subType)
subType
- the subtypepublic static ImmoniumIon getImmoniumIon(char residue)
residue
- the amino acid as charpublic String getName()
Ion
public CvTerm getPrideCvTerm()
Ion
getPrideCvTerm
in class Ion
public CvTerm getPsiMsCvTerm()
Ion
getPsiMsCvTerm
in class Ion
public int getSubType()
Ion
getSubType
in class Ion
public String getSubTypeAsString()
Ion
getSubTypeAsString
in class Ion
public static ArrayList<Integer> getPossibleSubtypes()
public NeutralLoss[] getNeutralLosses()
Ion
getNeutralLosses
in class Ion
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